Contacts of the helix formed by residues 183 - 195 (chain A) in PDB entry 3O9Z
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 183 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU 3.1 8.7 + - - -
179A ALA 3.0 16.1 + - - -
182A ILE* 1.3 77.5 - - - +
184A ILE* 1.3 65.1 + - - +
185A HIS 3.1 0.2 - - - -
186A PHE* 2.9 38.2 + - - -
187A PHE* 2.9 16.8 + - - -
225A LEU* 3.9 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LYS* 3.4 40.4 - - + -
102A PRO* 4.1 20.4 - - + -
128A LEU* 5.1 4.5 - - + -
179A ALA 3.2 2.7 + - - -
180A THR* 3.1 24.8 + - + +
181A ASN 4.3 0.7 - - - +
183A GLY* 1.3 76.9 - - - +
185A HIS* 1.3 66.4 + - - +
187A PHE* 4.5 4.0 - - + +
188A ASP* 2.8 32.0 + - + +
285A ALA* 3.6 40.8 - - + +
286A ILE* 3.9 16.6 - - + +
289A ALA* 4.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LYS* 3.7 23.6 - - + +
128A LEU* 5.2 7.3 - - - +
129A GLN* 3.4 35.2 + - - -
130A LEU* 3.6 24.5 + - + +
156A TYR* 3.7 26.7 - - + +
182A ILE 3.8 15.5 - - - +
183A GLY 3.0 0.6 + - - -
184A ILE* 1.3 79.2 - - - +
186A PHE* 1.3 58.5 + - - +
188A ASP* 3.8 4.1 - - - +
189A LEU* 3.0 25.5 + - - +
260A PHE* 3.8 6.7 - + - -
311A NAD 3.5 8.6 + - - -
312A AKG 2.8 33.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 4.8 0.7 - - - -
154A LEU* 3.5 33.2 - - + -
156A TYR* 3.7 33.2 - + + -
183A GLY* 2.9 28.0 + - - -
185A HIS* 1.3 77.8 - - - +
187A PHE* 1.3 99.5 + + - +
188A ASP 3.1 1.3 - - - -
189A LEU* 3.5 9.0 - - + +
190A LEU* 2.9 40.7 + - + +
223A TRP* 3.7 31.9 - + + -
224A PHE 5.1 0.7 - - - -
225A LEU* 3.8 24.7 - - + -
256A PHE* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ALA* 3.5 23.1 - - + -
183A GLY* 2.9 27.3 + - - +
184A ILE* 4.2 3.8 - - - +
186A PHE* 1.3 107.2 - + - +
188A ASP* 1.3 57.6 + - - +
190A LEU* 3.4 3.9 + - - +
191A ALA* 3.0 29.1 + - - +
214A LEU* 4.0 21.5 - - + -
223A TRP* 3.8 24.9 - + - -
285A ALA* 3.7 22.2 - - + +
288A VAL* 3.8 19.9 - - + +
289A ALA* 4.7 7.2 - - + -
292A LEU* 3.4 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 3.5 34.3 - - + +
130A LEU* 6.0 1.2 - - - +
131A ARG* 2.8 46.3 + - - +
184A ILE* 2.8 20.0 + - + +
185A HIS 3.8 2.8 - - - +
187A PHE* 1.3 75.3 - - - +
189A LEU* 1.3 59.7 + - - +
191A ALA* 3.3 2.7 + - - +
192A TRP* 2.9 30.1 + - - +
281A GLU 3.9 6.1 - - - +
282A ALA* 4.3 2.8 - - - -
285A ALA* 3.4 19.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 4.2 11.9 - - + +
131A ARG* 5.9 0.9 - - - -
136A LEU* 3.9 29.6 - - + -
154A LEU* 4.5 9.0 - - + -
185A HIS 3.0 18.2 + - - +
186A PHE* 3.2 7.4 + - - +
188A ASP* 1.3 76.5 + - - +
190A LEU* 1.3 59.7 + - - +
192A TRP* 3.3 28.4 + - + +
193A LEU* 3.0 51.3 + - + +
247A ILE* 4.3 17.0 - - + -
256A PHE* 4.1 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A VAL* 4.4 2.2 - - + -
154A LEU* 4.4 9.6 - - + -
186A PHE* 2.9 39.4 + - + +
187A PHE* 3.8 4.7 - - - +
189A LEU* 1.3 75.0 - - + +
191A ALA* 1.3 59.5 + - - +
193A LEU* 4.7 0.2 - - - -
194A PHE* 2.8 61.1 + - + +
195A GLY 3.8 0.2 + - - -
214A LEU* 3.8 20.2 - - + -
216A LEU* 3.8 13.9 - - + +
221A VAL* 3.8 33.2 - - + -
223A TRP* 5.3 0.4 - - + -
247A ILE* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ARG* 5.4 2.5 - - - +
187A PHE 3.0 17.8 + - - +
188A ASP* 3.8 7.9 - - - +
190A LEU* 1.3 76.1 - - - +
192A TRP* 1.3 61.6 + - - +
195A GLY* 2.8 36.2 + - - +
216A LEU* 5.3 0.7 - - - -
281A GLU 5.9 0.9 - - - +
284A GLU* 3.7 35.4 - - + -
285A ALA* 4.5 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU 4.1 4.0 - - - -
131A ARG* 3.4 83.1 - - + +
136A LEU 4.1 18.6 - - - -
137A LEU* 3.9 22.0 - - + -
140A LYS* 3.6 44.1 - - + +
188A ASP 2.9 17.8 + - - +
189A LEU* 3.5 31.2 - - + +
191A ALA* 1.3 79.4 - - - +
193A LEU* 1.3 71.0 + - + +
195A GLY 4.8 0.2 + - - -
277A PHE* 5.8 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU 4.5 1.8 - - - +
139A LEU* 4.4 11.2 - - + -
140A LYS* 3.4 45.9 - - + +
143A LEU* 4.2 9.9 - - + +
189A LEU* 3.0 39.2 + - + +
192A TRP* 1.3 89.4 - - + +
194A PHE* 1.3 90.1 + - + +
195A GLY 3.8 0.4 - - - -
247A ILE* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 3.9 39.3 - - + -
150A LYS* 4.5 5.4 - - + -
152A VAL* 3.8 28.0 - - + -
190A LEU* 2.8 44.7 + - + +
193A LEU* 1.3 94.0 - - + +
195A GLY* 1.3 63.0 + - - +
216A LEU* 3.7 13.8 - - + +
217A GLU* 3.5 6.1 + - - +
218A GLY* 2.8 51.7 + - - +
219A ALA* 3.5 16.2 - - + -
247A ILE* 4.3 2.2 - - + -
249A VAL* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ALA* 2.8 37.3 + - - +
192A TRP 4.8 0.2 + - - -
193A LEU 3.8 0.8 - - - -
194A PHE* 1.3 79.8 - - - +
196A ARG* 1.3 65.4 + - - -
197A ALA 3.8 0.7 + - - -
216A LEU* 4.2 7.8 - - - +
217A GLU* 3.5 10.1 - - - -
284A GLU* 4.3 2.0 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il